Joshua Marinnaci has started an
incubator project for the Misc API (org.jdesktop.jdic.misc)
for small buts of native functionality.
Currently this package contains the following APIs:

Alert API: indicate that a certain program (usually not the program currently focused) needs the user's attention.
On MacOSX this bounces the app's Dock icon. On Windows this flashes the task bar. Unix not supported yet.

Volume API: get, set, and monitor the system volume. (Mac OSX only)

DockMenu API: set a right click menu on the Dock icon (Mac OSX only)

Desktop background wallpaper API: set the background of the desktop. (Windows only)

Music Player API: Control the user's default music player (itunes, winamp, etc). (Mac iTunes currently supported).

Java 1.4 or later is required.

Jean-Marie Dautelle has released Javolution 4.0.2, a library that supports hard real-time compliant, multithreaded programming through concurrent algorithms, thread-safe collection classes, preallocated objects,
and object recycling. It also includes a forked SAX that replaces java.lang.String with CharArray and CharSequence "to avoid forcing dynamic object allocations."
Javolution is published under a BSD license.